This issue is a result of a Codex global code scan of deepmodeling/fpop at commit b05b337590c31a5237b2dcbd9c0833b841c08cd4.
Relevant code:
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confs = ["POSCAR-1","POSCAR-2","POSCAR-3"] |
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vasp_inputs = VaspInputs(0.4,'test_incar',{'Na':'test_potcar'},True) # kspacing incar potcar kgamma |
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prep_run_step = Step( |
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'prep-run-step', |
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template = steps, |
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parameters = { |
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'type_map' : ["Na"], |
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'prep_image_config' : prep_image_config, |
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'run_image_config' : run_image_config, |
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'inputs' : vasp_inputs, |
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'optional_input' : {"conf_format":"vasp/poscar"}, |
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'backward_list' : ["OUTCAR","CONTCAR"], |
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}, |
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artifacts = { |
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"confs" : upload_artifact(confs), |
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}, |
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confs = ["POSCAR-1","POSCAR-2","POSCAR-3"] |
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cp2k_inputs = Cp2kInputs('input.inp') # input files |
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prep_run_step = Step( |
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'prep-run-step', |
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template = steps, |
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parameters = { |
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'type_map' : ["Na"], |
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'prep_image_config' : prep_image_config, |
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'run_image_config' : run_image_config, |
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"log_name" : "output.log", |
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'inputs' : cp2k_inputs, |
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'optional_input' : {"conf_format":"vasp/poscar"}, |
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'backward_list' : ["output.log"], |
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}, |
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artifacts = { |
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"confs" : upload_artifact(confs), |
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}, |
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confs = ["POSCAR-1","POSCAR-2","POSCAR-3"] |
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abacus_inputs = AbacusInputs('INPUT',{'Na':'Na_ONCV_PBE-1.0.upf'}) |
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prep_run_step = Step( |
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'prep-run-step', |
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template = steps, |
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parameters = { |
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'type_map' : ["Na"], |
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'prep_image_config' : prep_image_config, |
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'run_image_config' : run_image_config, |
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'inputs' :abacus_inputs, |
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'optional_input' : {"conf_format":"vasp/poscar"}, |
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'backward_list' : ["OUT.ABACUS","log"], |
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}, |
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artifacts = { |
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"confs" : upload_artifact(confs), |
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}, |
Problem:
The example scripts refer to bundled input files with current-working-directory-relative paths such as POSCAR-1, test_incar, test_potcar, input.inp, INPUT, and Na_ONCV_PBE-1.0.upf.
Running an example from the repository root with a normal command such as:
python examples/vasp/preprunvasp.py
makes the script look for test_incar and POSCAR-1 in the repository root, even though those files live under examples/vasp/. The same pattern exists in the CP2K and ABACUS examples.
Expected behavior:
Each example should resolve local inputs from Path(__file__).resolve().parent, so the examples work regardless of the caller's current working directory.
This issue is a result of a Codex global code scan of
deepmodeling/fpopat commitb05b337590c31a5237b2dcbd9c0833b841c08cd4.Relevant code:
fpop/examples/vasp/preprunvasp.py
Lines 67 to 83 in b05b337
fpop/examples/cp2k/prepruncp2k.py
Lines 67 to 85 in b05b337
fpop/examples/abacus/preprunvasp.py
Lines 67 to 83 in b05b337
Problem:
The example scripts refer to bundled input files with current-working-directory-relative paths such as
POSCAR-1,test_incar,test_potcar,input.inp,INPUT, andNa_ONCV_PBE-1.0.upf.Running an example from the repository root with a normal command such as:
makes the script look for
test_incarandPOSCAR-1in the repository root, even though those files live underexamples/vasp/. The same pattern exists in the CP2K and ABACUS examples.Expected behavior:
Each example should resolve local inputs from
Path(__file__).resolve().parent, so the examples work regardless of the caller's current working directory.